SimOne@home, В 2 словах: проект грубо говоря изучает стабильность белков в разных к Налаштування

[nikelong]

SimOne@home

Оффсайт:
http://sim1.sytes.net/sim1/

Наша команда:
http://sim1.sytes.net/sim1/team_members.ph...credit&offset=0

About Simulation One
Simulation One, or SimOne@home (or even more easily SimOne), is a research project that uses Internet-connected computers to do research in the fields of science. You can participate by downloading and running a free program on your computer.

SimOne is completely created and managed by volonteers who believe in distributed computing. Our main base is of course the Boinc.Italy community from which we come. Currently we are testing the project studying the phenomenon of osmoprotection.

To investigate, here's to you some links:

Boinc.Italy web site
Osmoprotection
http://en.wikipedia.org/wiki/Osmoprotectant

Osmoprotectants

In nature, a variety of methods have been developed to allow many organisms to survive in extreme conditions such as, for example, high temperatures, high pressure or high salt concentrations. One of such method is the use of osmolytes, small molecules present even in very high concentrations in the cell fuid. Of these cosolvents in nature they are of two categories: osmoprotectant that stabilize the native structure of protein and denaturants that, on the contrary, destabilize the structure.

The mechanism of action of these molecules is still quite controversial. In fact, direct effects were observed in which the cosolvent acts directly by binding to specific sites of the protein, but were observed also indirect effects in which the cosolvent acts on the solvent changing its structure and properties and this in turn affects the protein stabilizing it or not.

The use of osmoprotectants and denaturing in the study of protein stability, both experimentally and in silico, it is very common. In particular, denaturants, such as urea, are widely used to investigate the stability of proteins, the effect of mutations on the stability and denaturation processes. Studies related to osmoprotectans are focused on the search for which molecules behave as osmoprotectans and which effects these have on proteins. Particularly studied is glycine betaine compound found in several bacterial species able to survive in extreme conditions, which is widely used in the simulations for the study of osmoprotectans. Other molecules known as osmoprotectans are some polyalcohols such as trehalose, some amino acids such as proline and betaines as the aforementioned glycine betaine.

The aim of this project is the development of a computational method capable of determining whether a molecule has an osmoprotective or denaturant effect, based on data obtained by evaluating the free energy of the process of unfolding of some polypeptide model.

The expected results for this phase should be as follows:
given a certain amount of free energy variation for the unfolding of the polypeptide in water alone, we expect a value of free energy variation is greater in cases in which the peptide was tested in the presence of osmoprotectans and less in presence of denaturants. An osmoprotectans should in fact increase the stability, and thus decrease the free energy, of folded state and this would correspond to an increase in free energy variation between folded and unfolded state, while a denaturant should decrease the stability of the folded state and then decreasing the variation free energy.

The polypeptides that are studied are two: a beta hairpin and the protein 1L2Y. The beta-hairpin was chosen as an example of beta-sheet secondary structure (length: 16 amino acids). The protein 1L2Y was chosen instead as an example of alpha helix. Special features of this protein, also called 'tpr-cage', is the fact, although very small (only 20 amino acids), it possess defined tertiary structure.

The co-solvents that are used are four: glycine betaine (GBE) and Ectoin (ECT) as osmoprotectans and urea (URE) and guanidinium chloride (GUA) as denaturant. All four compounds are fairly standard, used widely for studies in this field, both in computational and experimental.

The computational techniques that are used for calculating the free energy of unfolding are, for the moment, the umbrella sampling and Jarzynski's equation.

В 2 словах: проект грубо говоря изучает стабильность белков в разных критических условиях (температура, давление, соли)

Це повідомлення відредагував nikelong: Mar 17 2012, 17:29